(setq absent-essential-compounds '(ALA ASP DTTP))
(setq unproduceable-essential-compounds '(DATPDGTP))
(setq minimal-nutrient-set
'(ASN GLY CTP UDP-GALACTOSE LYS UDP-GLUCOSE
  ADP-L-GLYCERO-D-MANNO-HEPTOSE ARG TRP SER FRUCTOSE-6P THR CYS GTP GLN
  UTP UDP RIBULOSE-5P GLYCEROL-3P CDPDIACYLGLYCEROL 3-OHMYRISTOYL-ACP
  WATER DIACETYLCHITOBIOSE-6-PHOSPHATE VAL TYR PHE LEU ILE MET
  MESO-DIAMINOPIMELATE GLT L-ALPHA-ALANINE UDP-N-ACETYL-D-GLUCOSAMINE
  PHOSPHO-ENOL-PYRUVATE ATP D-ALANINE UNDECAPRENYL-P PRO HIS GLC-1-P
  TTP NADPH))
(setq on-genes
      '(EG10566 EG11789 EG10775 EG10781 G7164 EG10220 G6428 G6455 EG10221
	  EG11326 EG10137 G7841 EG10810 EG11539 EG11701 G6358 EG10219 EG10994
	  EG11418 G7663 G7662 EG10518 UNKNOWN EG10706 EG11608 EG10546 EG10138
	  EG10265 EG10545 EG10316 EG10144 EG10621 EG10620 EG11204 EG10619
	  EG11358 EG11205 EG10622 EG10213 EG10604 EG10623 EG11979 EG12412
	  EG11978 EG12411))
(setq reversibles
      '(DCTP-DEAM-RXN CYTIDEAM2-RXN))

(pathway-tools-file "minimal-nutrients.txt" minimal-nutrient-set)
(pathway-tools-file "on-genes.txt" on-genes)
(pathway-tools-file "reversibles.txt" reversibles)
(pathway-tools-file "all.txt" (append reversibles on-genes minimal-nutrient-set))